The Blastocystis PubMLST database now has a new look!

Thanks to Keith Jolley and colleauges, the PubMLST site now has a new look! Why not try and visit the Blastocystis section? It's available here. 

The Blastocystis database has mostly been used to identify whether subtypes that are shared between humans are animals reflect the same strains or not based on intra-subtype genetic variation (allele analysis), for which is works quite well. For this purpose, you should use DNA sequences reflecting the barcode region.

 You can query a single sequence or a whole batch of sequences. On the landing page, simply press 'Typing' and then opt for 'Single sequence' or 'Batch seqeunces', depending on what you want to analyse.

It's our ambition to expand the database with more subtype alleles, since this will allow all Blastocystis researchers interested in Blastocystis epidemiology to query their barcode sequences against a curated, standardised database. However, the genetic universe of Blastocystis is rapidly expanding, so it can be difficult to keep up! 

This site works best with Sanger sequences, or, possibly, consensus sequences generated based on next-generation sequencing of the 5'-end of the SSU rRNA gene of Blastocystis; we still haven't very much experience with the latter.

 

2nd International Blastocystis Conference Wrap-Up - Part II

So, a lot of people would like to know about the take-home messages from the recent 2nd International Blastocystis Conference in Bogotá. There were many, and I might develop one more post to make room for more.

The first - and most important - thing I'd like to emphasise is that the community interested in Blastocystis is growing. And we're seeing a clearly multidisciplinary approach to studying the parasite. I think that this is what we need. The initial ideas about having Blastocystis-specific conference were developed by Funda Dogruman-Al and myself, and we both have a background in clinical microbiology. We have realised that in order to make sense of Blastocystis in a clinical microbiology (and infectious disease) context, we need research input from bordering fields, such as biology (genomics, cell biology, etc.), veterinary medicine (host specificity and impact of Blastocystis on animal health), gastroenterology (connection to microbiota and the extent of Blastocystis being involved in functional and inflammatory bowel diseases), bioinformatics (processing NGS data such as those pertaining to the profiling of gut microbiota communities), and ecology (people who are used to study interactions between organisms). At the conference, I believe that all (or at least most) of these fields were represented.

I was also thrilled to realise that many researchers have now adapted to the subtype terminology, - and even the allele terminology appears to be useful and pragmatic.

Status on the Blastocystis genome project. Slide by Andrew Roger.

Andrew Roger highlighted that the genomes of Blastocystis are more different than the genomes of human and mouse! Well-annotated genomes are available for ST1, ST4, and ST7, while draft genomes are available for subtypes 2, 3, 6, 8 and 9. 

 

What use are genomes? Summary provided by Andrew Roger.

Animal experimental modelling is possible. We know that rats can be colonised/infected by Blastocystis ST1 strain from a human and shed cysts in stool for more than one year.

Blastocystis is one of the few parasites that are really easy to culture and easy to get by. If we can learn to induce cysts in culture, these can be separated by sucrose gradient centrifugation or other methods and used for inoculation into volunteers, pigs, or rats, for instance. This can be used to study the impact of Blastocystis on the host, including immune system and gut microbiota. Baseline microbiota profiling is necessary prior to inoculation to know about the background variation in study individuals.

In terms of Blastocystis and gut microbiota: Since we published our conspicuous observations in 2015, many researchers have now corroborated our findings: Blastocystis is typically linked to increased microbiota richness and diversity; - something, which is generally considered a benefit and which is linked not only to gut health, but also to leanness. Especially the negative association between Blastocystis and Bacteroides has been highlighted by many now. It will be very interesting to learn why this is so. It also seems that Blastocystis are more common in individuals with a gut microbiota dominated by strictly anaerobes rather than facultative aerobes.

Faecal microbiota transplantaion (FMT): The recommendation of excluding FMT donors based on the finding of Blastocystis came up many times and was discussed in the context of the microbiota studies. It appear relevant to investigate further whether FMT donors should really be dismissed if they are Blastocystis-positive.

Some of the take home messages from Raul Tito Tadeo's talk.

In many animal groups, Blastocystis is a very common finding. These include mostly omnivores or herbivores. On the contrary, Blastocystis is very rare in strict carnivores, with no consistency in subtype distribution, indicating that these animals are not natural hosts of Blastocystis.The Blastocystis incidentially found in these hosts might stem from the prey that they have eaten.

Finally, I wish to highlight that there are excellent resources available from the pre-conference workshop, including an R script for microbiota analysis, and some tools for Blastocystis genome annotation. Please visit my previous blog post for links to these.

We cannot totally dismiss pathogenicity of Blastocystis; if existing, it may involve both strain- and host-specific factors.

And.... it's out: The time and venue for the 3rd International Blastocystis Conference will be Crete in 2021 (possibly June), with Eleni Gentekaki and Anastasios Tsaousis being involved in both the scientific and local organising committees... ! Please mark you calendars!

Andrew Roger, Raul Tito Tadeo, Kevin Tan and myself (taking the picture) enjoying some Club Colombia.

Website for 2nd International Blastocystis Conference is now live!

I'm happy to be able to point your attention towards the website for the 2nd International Blastocystis Conference in Bogotá in October 2018. You can access the website here.

On this site, you'll find information about the venue, the preliminary programme, speakers, registration, and sponsors. You will also find some information about Bogotá.

Please visit the website on a regular basis for potential updates/changes.

See you there!

Trends in Blastocystis Research

I thought I'd post two current conference abstracts to exemplify some of the trends in  Blastocystis research.

The first is from Dr Pauline D Scanlan, who will be speaking at 15th International Congress of Protistology currently taking place in Prague. Go here for more info about the meeting.

In the symposium 'The eukaryome, bringing protists into the spotlight of microbiome research' taking place today, Pauline will be giving a talk with the title:

Inter-Kingdom Interactions in the human gut microbiome-the prevalence of the intestinal protist Blastocystis is linked to host age, antibiotic use and gut bacterial diversity and composition

and the abstract reads like this:

The human gut is host to a complex microbial ecosystem that plays a central role in host health. In addition to bacteria, viruses and archaea, the gut microbiota includes a diversity of fungal and protist species that are collectively referred to as the gut ‘eukaryome’. Although research into the gut eukaryome is in its infancy, emerging data indicates that the intestinal protist Blastocystis is perhaps the most common member of the human gut eukaryome worldwide. Despite its association with intestinal disease, asymptomatic carriage is common with Blastocystis frequently observed in surveys of the healthy adult gut microbiome. Furthermore, Blastocystis is less prevalent in chronic diseases such as Irritable Bowel Syndrome compared to healthy controls. Antibiotic administration significantly reduces Blastocystis prevalence rates between case and controls groups with the reduction in Blastocystis prevalence in the antibiotic treated group possibly due to direct effects on Blastocystis and/or secondary loss due to loss of bacteria that Blastocystis interacts with. In support of this latter hypothesis, data showing correlations between the presence of Blastocystis and specific features of the bacterial component of the gut microbiome (high diversity and a specific bacterial composition) are suggestive of inter-kingdom interactions between bacteria and Blastocystis in the gut microbiome. Blastocystis is less prevalent in infant populations relative to contemporaneous adult populations indicating that Blastocystis is not adapted to the infant gut. Given the difference in microbiome composition and diversity in infants compared to adults perhaps Blastocystis requires a more adult-like gut microbiome for successful colonisation. Collectively, emerging data suggests that successful colonisation of the gut by Blastocystis is linked to the composition and diversity of the bacterial fraction of human gut microbiome. Consequently, interactions between Blastocystis and bacteria in the gut microbiome may account for some of the variation in prevalence rates observed across age, health and geography.

 
Along similar lines, I will be giving a talk at the EMBO conference 'Anaerobic protists: Integrating Parasitology with mucosal microbiota and immunology' running from 31 AUG to 03 SEP in Newcastle, UK. You can read about the conference here.

The title and abstract of my talk are as follows:

The diversity of the most common intestinal protists, Blastocystis and Dientamoeba, and their interactions with the microbiota: what role in health and disease?

The integration of DNA-methods in Clinical Microbiology has enabled a more detailed and accurate snapshot of the protists colonising and infecting our guts. Parasites like Blastocystis and Dientamoeba are much more common than previously known, when detection relied mainly on microscopy of faecal concentrates and smears only.

While Dientamoeba isolated from humans exhibits very little genetic variation across the small subunit ribosomal gene, Blastocystis displays a perplexing amount of genetic heterogeneity, and nine subtypes, which are arguably separate species, have been found in humans. Subtypes 1 to 4 account for about 95% of human Blastocystis carriage.

It is expected that over 1 billion people are colonised by Blastocystis, and based on DNA-based detection, prevalence figures of up to 100% have been reported in developing countries. Conversely, the prevalence of Blastocystis appears relatively low in e.g. the US, and it has been suggested that the low prevalence is indicative of the defaunation of indviduals adapting a Westernized life style.

In a developed country like Denmark, the prevalence of Blastocystis and Dientamoeba is highest in individuals without gastrointestinal, while the prevalence of these parasites is lower in patients with functional and organic bowel disease, suggesting that these parasites are in fact markers of gastrointestinal health.

This is also in part exemplified by recent independent data linking high gut microbiota diversity to the presence of these parasites. Certain bacterial populations appear to be linked to parasite carriage, and studies are emerging that try to look into the association between these parasites and the remaining gut microbiota.

Moreover, higher age appears to be linked to Blastocystis colonisation. Blastocystis is more common in older children and adults, while in younger children, Dientamoeba is much more common.

Whether these parasites are able to modulate gut microbiota structure and function remains unknown, and it also remains to be demonstrated whether certain microbiota communities and/or metabolites are required for successful establishment of these parasites. More research data on these topics will inform future advances in probiotics in particular and gut microbiota manipulation in general.

 Thanks for your time.